Multidimensional annotation of the Escherichia coli K-12 genome Export

@article{citeulike:2191612, abstract = {The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns biochemical functions to 76\%, and 66\% of all genes had their functions determined experimentally. EcoCyc assigns E. coli genes to Gene Ontology and to MultiFun. Seventy-five percent of gene products contain reviews authored by the EcoCyc project that summarize the experimental literature about the gene product. EcoCyc information was derived from 15 000 publications. The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes. A comparison to genome annotations for other model organisms shows that the E. coli genome contains the most experimentally determined gene functions in both relative and absolute terms: 2941 (66\%) for E. coli, 2319 (37\%) for Saccharomyces cerevisiae, 1816 (5\%) for Arabidopsis thaliana, 1456 (4\%) for Mus musculus and 614 (4\%) for Drosophila melanogaster. Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks. 10.1093/nar/gkm740}, author = {Karp, Peter D. and Keseler, Ingrid M. and Shearer, Alexander and Latendresse, Mario and Krummenacker, Markus and Paley, Suzanne M. and Paulsen, Ian and Collado-Vides, Julio and Gama-Castro, Socorro and Peralta-Gil, Martin and Santos-Zavaleta, Alberto and Penaloza-Spinola, Monica I. and Bonavides-Martinez, Cesar and Ingraham, John}, citeulike-article-id = {2191612}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkm740}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/35/22/7577}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17940092}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17940092}, day = {3}, doi = {10.1093/nar/gkm740}, journal = {Nucl. Acids Res.}, keywords = {ecocyc}, month = {December}, number = {22}, pages = {7577--7590}, posted-at = {2009-01-29 22:13:59}, priority = {2}, title = {Multidimensional annotation of the Escherichia coli K-12 genome}, url = {http://dx.doi.org/10.1093/nar/gkm740}, volume = {35}, year = {2007} }

TY - JOUR ID - citeulike:2191612 L3 - citeulike-article-id:2191612 N2 - The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns biochemical functions to 76%, and 66% of all genes had their functions determined experimentally. EcoCyc assigns E. coli genes to Gene Ontology and to MultiFun. Seventy-five percent of gene products contain reviews authored by the EcoCyc project that summarize the experimental literature about the gene product. EcoCyc information was derived from 15 000 publications. The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes. A comparison to genome annotations for other model organisms shows that the E. coli genome contains the most experimentally determined gene functions in both relative and absolute terms: 2941 (66%) for E. coli, 2319 (37%) for Saccharomyces cerevisiae, 1816 (5%) for Arabidopsis thaliana, 1456 (4%) for Mus musculus and 614 (4%) for Drosophila melanogaster. Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks. 10.1093/nar/gkm740 IS - 22 JF - Nucl. Acids Res. EP - 7590 TI - Multidimensional annotation of the Escherichia coli K-12 genome VL - 35 SP - 7577 KW - ecocyc AU - Karp, Peter AU - Keseler, Ingrid AU - Shearer, Alexander AU - Latendresse, Mario AU - Krummenacker, Markus AU - Paley, Suzanne AU - Paulsen, Ian AU - Collado-Vides, Julio AU - Gama-Castro, Socorro AU - Peralta-Gil, Martin AU - Santos-Zavaleta, Alberto AU - Penaloza-Spinola, Monica AU - Bonavides-Martinez, Cesar AU - Ingraham, John PY - 2007/12/03/ UR - http://dx.doi.org/10.1093/nar/gkm740 ER -